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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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Representative site 3i20:A2925, See in JSmolMgRNA representative site for type OB Click on the image to toggle views


Site type: Ob

Schematic drawing for
Ob
MgRNA type OB
List of all 468 Mg2+ binding sites with the site type Ob in RNA crystal structures in the benchmark dataset (switch to full dataset)
Sites in the table can be ordered by the following fields by clicking the column header: "PDB ID" or "Mg2+ ID"
Page 5 of 19 | | | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
2qp1 B2984 Ob C:B2499(O2) B3905, B3906, B3907, B3908, B3909 G:B2032 C:B2055, U:B2500, G:B2032, G:B2454, A:B2453
2qp1 B2972 Ob U:B746(O4) B3853, B3854, B3855, B3856, D408 U:B744, C:B2610, C:B2611
2r8s R1003 Ob G:R188(O6) R1010, R1011, R1012, R1013, R1014 U:R182, U:R168, A:R183, C:R166, C:R165 A:R183
2z4k A1576 Ob G:A1370(O6) A1765, A1766, A1767, A1768, A1769 U:A1348 G:A1371, U:A1372, U:A1351
2z4k A1603 Ob G:A1417(O6) A1892, A1893, A1894, A1895, A1896 G:A1416, G:A1415 G:A1482, G:A1416
2z4l B2940 Ob C:B2499(O2) B3180, B3181, B3182, B3183, B3184 C:B2055, U:B2500, G:B2032, G:B2454, A:B2453
2z4l B2937 Ob U:B746(O4) B3166, B3167, B3168, B3169, D210 C:B2610, C:B2611, U:B744 G:B745
2z4m A1579 Ob G:A1370(O6) A1785, A1786, A1787, A1788, A1789 U:A1351, G:A1371
2z4m A1604 Ob G:A1417(O6) A1901, A1902, A1903, A1904, A1905 G:A1415 G:A1482, G:A1416
2z4n B2985 Ob C:B2499(O2) B3399, B3400, B3401, B3402, B3403 C:B2499 C:B2055, U:B2500, G:B2032, G:B2454
354d B204 Ob G:B98(O6) A319, A323, B320, B321, B322 G:A76, G:A76, C:B97 G:A75
3df1 A2349 Ob U:A1358(O4) A4350, A4351, A4352, A4353, A4354 C:A1359, A:A1357
3df1 A2355 Ob G:A1417(O6) A4356, A4357, A4358, A4359, A4360 G:A1416, G:A1415 G:A1416, G:A1482
3df1 A2109 Ob G:A1050(O6) A4110, A4111, A4112, A4113, A4114 C:A1051, C:A1208, G:A1207
3df2 B3206 Ob C:B2499(O2) B4207, B4208, B4209, B4210, B4211 G:B2032 C:B2055, U:B2500, G:B2032, G:B2454, A:B2453
3df2 B3188 Ob U:B746(O4) B4189, B4190, B4191, B4192, D4193 U:B744, C:B2610, C:B2611 G:B745
3df3 A2366 Ob G:A1417(O6) A4367, A4368, A4369, A4370, A4371 G:A1415 G:A1416
3df4 B3468 Ob C:B2499(O2) B4469, B4470, B4471, B4472, B4473 G:B2032 C:B2055, U:B2500, G:B2032, G:B2454, A:B2453
3i1n A2925 Ob U:A746(O4) A3147, A3148, A3149, A3150, A3151 U:A744, C:A2611, C:A2610 G:A745
3i1n A3036 Ob U:A2593(O4) A3635, A3636, A3637, C776, C778 G:A2592 G:A2592, C:A2594, G:A2599
3i1n A2975 Ob C:A2499(O2) A3377, A3378, A3379, A3380, A3381 G:A2032 C:A2055, U:A2500, G:A2454, G:A2032
3i1n A3004 Ob U:A2419(O4) A3515, A3516, A3517, 3626, 3629 A:A2418
3i1n A2992 Ob G:A1125(O6) A3453, A3454, A3455, A3456, A3457 A:A1028 A:A1126
3i1n B122 Ob U:B95(O4) B656, B657, B658, B659, B660 U:B80, G:B96
3i1o A1550 Ob G:A1417(O6) A1667, A1668, A1669, A1670, A1671 G:A1415, G:A1416, G:A1482

Site type used in the classification is a string abbreviation of ligand composition in Mg2+ coordination sphere
Abbreviations
used for Mg2+
"Site type"		 Mg2+ inner-sphere ligands Geometry for inner-sphere OP Mg2+ outer-sphere moieties
Oph phosphate oxygen (OP1/OP2)
Or ribose oxygen (O2'/O4')
     or oxygen bridging phosphate and ribose (O3'/O5')
Ob nucleobase oxygen      Nb nucleobase nitrogen 		cis- two OP ligands adopt cis- isoform
trans- two OP ligands adopt trans- isoform
fac- three OP ligands adopt fac- isoform
mer- three OP ligands adopt mer- isoform 		Pout phosphate moiety
Rout ribose moiety
Bout nucleobase moiety
Reference: Zheng H, Shabalin IG, Handing KB, Bujnicki JM, Minor W. (2015) Magnesium binding architectures in RNA crystal structures: validation, binding preferences, classification, and motif detection. Nucleic Acid Research 43(7):3789-801 [Pubmed].

Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
For any help please contact <dust@iwonka.med.virginia.edu>